Open a terminal.
If you don't already have a conda software manager in the Linux box, install one with all the defaults:
The metadata is updated as new samples are made public, so every few days you'll want to refresh your instance by running this command from inside the top level directory of ncov:
The critical step at this stage is to make sure each FastA record's ID (everything between ">" and the first space or new line in the description line) matches the names NextStrain has given to each sequence in the file data/metadata.tsv. This is left as an exercise to the reader as the sequence data you have access to will be ever changing. Often you will need to change a '/' to a '-', remove the "BetaCov/" ID prefix, remove the '_EPI####' suffix from GISAID downloads, etc.
If you had a new sequence of your own that you wanted to add, you would append it to the data/sequences.fasta file, and add a line to the data/metadata.tsv with the relevant information. Note that this will prevent updates with git pull in the future, as git does not want to clobber your changes. Tip: Save the extra lines you wrote in another file for safe keeping, so you can delete data/metadata.tsv and auspice/ncov.json, then successfully run git pull for code updates.